| Environment Variable | Description |
|---|---|
OCX_SAMPLE_FILENAME | The normalized filename of the FASTA/Q file that was uploaded to One Codex. This will correspond to the name of the file that is injected into the working directory for your workflow. |
OCX_SAMPLE_NAME | The name of the Sample in One Codex. This might be different from the filename if the user has edited the Sample metadata. |
OCX_SAMPLE_UUID | The UUID of the Sample in One Codex. This is a globally unique identifier for the Sample that was used as input for the workflow. |
OCX_ANALYSIS_UUID | The UUID of the current Analysis in One Codex. This is a globally unique identifier for the current workflow run on a particular sample with the specific set of input parameters. This can be used to globally identify a particular instance of an Analysis in One Codex. |
OCX_CPU_REQUEST | The number of CPUs requested for your workflow. Pass this to multi-threaded tools so they use all the CPUs available to the run. |
OCX_INSTRUMENT_VENDOR | The name of the sample’s instrument vendor (e.g., “Illumina”, “Oxford Nanopore”). |
OCX_IS_LONG_READ | "true" if the sample is detected to be from a long read sequencer (e.g., PacBio or ONT); "false" otherwise. |
OCX_DEPENDENCY_UUIDS | Space-separated list of Analysis UUIDs that the current analysis depends on. |
Workflow Parameters as Environment Variables
Any parameters that are defined for your workflow either as part of the workflow definition or by the user at the time of analysis kickoff are injected into the execution environment as environment variables.What’s next? Learn the specifics of Nextflow on One Codex.